In the present study, a couple of simple models were presented to estimate the energy of individual hydrogen bonds in traditional base pairs. In this regard, formamide and formamidine dimers and a set of their derivatives with different functional groups such as F, Cl, Br, CH3, CN, ethynyl, nitroso, and vinyl were considered. All of these structures are optimized by M06-2X and MP2 methods in conjunctions with 6–311 +  + G(d,p) basis set. The computational results showed that the hydrogen bond energy in the first method is higher than the MP2 and also the NHN interactions are stronger than the corresponding NHO ones. Moreover, the relationships between the energy hydrogen bonds and all of the geometrical, topological, and molecular orbital descriptors were also explored. The absolute values of the correlation coefficient (R2) indicated the best linear relationships between the electron density at the hydrogen bond critical point (ρ(r)) and the energy of NHN (R2 = 0.98) and NHO (R2 = 0.82) hydrogen bonds. Based on these equations, it was found that the orders of calculated individual HB energies of the Watson–Crick base pairs are completely similar to the compliance constant model of Gruenberg. Finally, the energy of individual bonds in a set of usual base pairs was evaluated and compared with their complexation energies. The slight difference between ƩEHB and ΔEComp reflects the high accuracy of the proposed models and equations.

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